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Added ChemSpider InChIKey resolution functionality
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <classpath> | ||
| <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/> | ||
| <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/> | ||
| <classpathentry kind="src" path="src"/> | ||
| <classpathentry kind="output" path="bin"/> | ||
| </classpath> |
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>net.bioclipse.chemspider</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| <buildCommand> | ||
| <name>org.eclipse.jdt.core.javabuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>org.eclipse.pde.ManifestBuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>org.eclipse.pde.SchemaBuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| </buildSpec> | ||
| <natures> | ||
| <nature>org.eclipse.pde.PluginNature</nature> | ||
| <nature>org.eclipse.jdt.core.javanature</nature> | ||
| </natures> | ||
| </projectDescription> |
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| Manifest-Version: 1.0 | ||
| Bundle-ManifestVersion: 2 | ||
| Bundle-Name: Bioclipse ChemSpider Integration | ||
| Bundle-SymbolicName: net.bioclipse.chemspider; singleton:=true | ||
| Bundle-Version: 2.4.0.RC2_1 | ||
| Bundle-Activator: net.bioclipse.chemspider.Activator | ||
| Bundle-Vendor: The Bioclipse Project | ||
| Export-Package: net.bioclipse.chemspider, net.bioclipse.chemspider.business | ||
| Require-Bundle: org.eclipse.ui, | ||
| org.eclipse.core.runtime, | ||
| net.bioclipse.core, | ||
| net.bioclipse.scripting, | ||
| org.springframework.bundle.spring.aop, | ||
| net.sf.cglib, | ||
| org.springframework.osgi.aopalliance.osgi, | ||
| org.eclipse.core.resources, | ||
| net.bioclipse.cdk.business | ||
| Bundle-RequiredExecutionEnvironment: JavaSE-1.6 | ||
| Import-Package: org.apache.log4j | ||
| Bundle-ActivationPolicy: lazy |
68 changes: 68 additions & 0 deletions
68
plugins/net.bioclipse.chemspider/META-INF/spring/context.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
|
|
||
| <beans xmlns="http://www.springframework.org/schema/beans" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xmlns:osgi="http://www.springframework.org/schema/osgi" | ||
| xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd | ||
| http://www.springframework.org/schema/osgi http://www.springframework.org/schema/osgi/spring-osgi.xsd"> | ||
|
|
||
| <osgi:service id="javaChemspiderManagerOSGI" | ||
| ref="javaChemspiderManager" | ||
| interface="net.bioclipse.chemspider.business.IJavaChemspiderManager" /> | ||
|
|
||
| <osgi:service id="javaScriptChemspiderManagerOSGI" | ||
| ref="javaScriptChemspiderManager" | ||
| interface="net.bioclipse.chemspider.business.IJavaScriptChemspiderManager" /> | ||
|
|
||
| <osgi:reference id="recordingAdvice" | ||
| interface="net.bioclipse.recording.IRecordingAdvice" /> | ||
|
|
||
| <osgi:reference id="javaManagerDispatcherAdvisor" | ||
| interface="net.bioclipse.managers.business.IJavaManagerDispatcherAdvisor" /> | ||
|
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||
| <osgi:reference id="javaScriptManagerDispatcherAdvisor" | ||
| interface="net.bioclipse.managers.business.IJavaScriptManagerDispatcherAdvisor" /> | ||
|
|
||
| <osgi:reference id="wrapInProxyAdvice" | ||
| interface="net.bioclipse.recording.IWrapInProxyAdvice" /> | ||
|
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| <bean id="recordingAdvisor" | ||
| class="org.springframework.aop.support.RegexpMethodPointcutAdvisor"> | ||
| <property name="advice" ref="recordingAdvice" /> | ||
| <property name="pattern" value=".*" /> <!-- See also class implementation --> | ||
| </bean> | ||
|
|
||
| <bean id="ChemspiderManagerTarget" | ||
| class="net.bioclipse.chemspider.business.ChemspiderManager"> | ||
| </bean> | ||
|
|
||
| <bean id="javaScriptChemspiderManager" | ||
| class="org.springframework.aop.framework.ProxyFactoryBean"> | ||
| <property name="target" | ||
| ref="ChemspiderManagerTarget" /> | ||
| <property name="proxyInterfaces" | ||
| value="net.bioclipse.chemspider.business.IJavaScriptChemspiderManager" /> | ||
| <property name="interceptorNames" > | ||
| <list> | ||
| <value>recordingAdvisor</value> | ||
| <value>wrapInProxyAdvice</value> | ||
| <value>javaScriptManagerDispatcherAdvisor</value> | ||
| </list> | ||
| </property> | ||
| </bean> | ||
|
|
||
| <bean id="javaChemspiderManager" | ||
| class="org.springframework.aop.framework.ProxyFactoryBean"> | ||
| <property name="target" | ||
| ref="ChemspiderManagerTarget" /> | ||
| <property name="proxyInterfaces" | ||
| value="net.bioclipse.chemspider.business.IJavaChemspiderManager" /> | ||
| <property name="interceptorNames" > | ||
| <list> | ||
| <value>recordingAdvisor</value> | ||
| <value>wrapInProxyAdvice</value> | ||
| <value>javaManagerDispatcherAdvisor</value> | ||
| </list> | ||
| </property> | ||
| </bean> | ||
| </beans> |
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| source.. = src/ | ||
| output.. = bin/ | ||
| bin.includes = plugin.xml,\ | ||
| META-INF/,\ | ||
| . |
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <?eclipse version="3.4"?> | ||
| <plugin> | ||
|
|
||
| <extension | ||
| point="net.bioclipse.scripting.contribution"> | ||
| <scriptContribution | ||
| service="net.bioclipse.chemspider.business.ChemspiderManagerFactory" | ||
| id="net.bioclipse.chemspider.business.ChemspiderManager"> | ||
| </scriptContribution> | ||
| </extension> | ||
|
|
||
| </plugin> |
105 changes: 105 additions & 0 deletions
105
plugins/net.bioclipse.chemspider/src/net/bioclipse/chemspider/Activator.java
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| /******************************************************************************* | ||
| * Copyright (c) 2010 Egon Willighagen <egon.willighagen@gmail.com> | ||
| * | ||
| * All rights reserved. This program and the accompanying materials | ||
| * are made available under the terms of the Eclipse Public License v1.0 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contact: http://www.bioclipse.net/ | ||
| ******************************************************************************/ | ||
| package net.bioclipse.chemspider; | ||
|
|
||
| import net.bioclipse.chemspider.business.IChemspiderManager; | ||
| import net.bioclipse.chemspider.business.IJavaChemspiderManager; | ||
| import net.bioclipse.chemspider.business.IJavaScriptChemspiderManager; | ||
|
|
||
| import org.apache.log4j.Logger; | ||
| import org.eclipse.ui.plugin.AbstractUIPlugin; | ||
| import org.osgi.framework.BundleContext; | ||
| import org.osgi.util.tracker.ServiceTracker; | ||
|
|
||
| /** | ||
| * The Activator class controls the plug-in life cycle | ||
| */ | ||
| public class Activator extends AbstractUIPlugin { | ||
|
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| private static final Logger logger = Logger.getLogger(Activator.class); | ||
|
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| // The shared instance | ||
| private static Activator plugin; | ||
|
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| // Trackers for getting the managers | ||
| private ServiceTracker javaFinderTracker; | ||
| private ServiceTracker jsFinderTracker; | ||
|
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| public Activator() { | ||
| } | ||
|
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| public void start(BundleContext context) throws Exception { | ||
| super.start(context); | ||
| plugin = this; | ||
| javaFinderTracker | ||
| = new ServiceTracker( context, | ||
| IJavaChemspiderManager.class.getName(), | ||
| null ); | ||
|
|
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| javaFinderTracker.open(); | ||
| jsFinderTracker | ||
| = new ServiceTracker( context, | ||
| IJavaScriptChemspiderManager.class.getName(), | ||
| null ); | ||
|
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| jsFinderTracker.open(); | ||
| } | ||
|
|
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| public void stop(BundleContext context) throws Exception { | ||
| plugin = null; | ||
| super.stop(context); | ||
| } | ||
|
|
||
| /** | ||
| * Returns the shared instance | ||
| * | ||
| * @return the shared instance | ||
| */ | ||
| public static Activator getDefault() { | ||
| return plugin; | ||
| } | ||
|
|
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| public IChemspiderManager getJavaChemspiderManager() { | ||
| IChemspiderManager manager = null; | ||
| try { | ||
| manager = (IChemspiderManager) | ||
| javaFinderTracker.waitForService(1000*10); | ||
| } | ||
| catch (InterruptedException e) { | ||
| throw new IllegalStateException( | ||
| "Could not get the Java ChemspiderManager", | ||
| e ); | ||
| } | ||
| if (manager == null) { | ||
| throw new IllegalStateException( | ||
| "Could not get the Java ChemspiderManager"); | ||
| } | ||
| return manager; | ||
| } | ||
|
|
||
| public IJavaScriptChemspiderManager getJavaScriptChemspiderManager() { | ||
| IJavaScriptChemspiderManager manager = null; | ||
| try { | ||
| manager = (IJavaScriptChemspiderManager) | ||
| jsFinderTracker.waitForService(1000*10); | ||
| } | ||
| catch (InterruptedException e) { | ||
| throw new IllegalStateException( | ||
| "Could not get the JavaScript ChemspiderManager", | ||
| e ); | ||
| } | ||
| if (manager == null) { | ||
| throw new IllegalStateException( | ||
| "Could not get the JavaScript ChemspiderManager"); | ||
| } | ||
| return manager; | ||
| } | ||
| } |
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